Masks recombinant regions in an alignment based on ClonalFrameML output
Option to draw SVG of recombinant regions
Jason Kwong (@kwongjc)
GitHub: kwongj
$ cfml-maskrc.py -h
usage:
cfml-maskrc.py --aln FASTA --out OUTFILE <CFML_PREFIX>
Script to mask recombination from ClonalFrameML output and draw SVG of recombinant regions
positional arguments:
CFML_PREFIX prefix used for CFML output files (required)
optional arguments:
-h, --help show this help message and exit
--aln FASTA multiFASTA alignment used as input for CFML (required)
--out OUTFILE output file for masked alignment (default="maskrc.aln")
--symbol ? symbol to use for masking (default="?")
--regions FILE output recombinant regions to file
--svg FILE draw SVG output of recombinant regions and save as specified file
--svgsize WIDExHIGH specify width and height of SVG in pixels (default="800x600")
--svgorder FILE specify file containing list of taxa (1 per line) in desired order
--svgcolour COLOUR specify colour of recombination regions in HEX format (default=black)
--consensus add consensus row of recombination hotspots
--version show program's version number and exit
Requires:
Options:
--out OUTFILE
--symbol ?
--regions FILE
--svg FILE
--svgsize WIDTHxHEIGHT
--svgorder FILE
--svgcolour COLOUR
--consensus
Please submit via the GitHub issues page: https://github.com/kwongj/cfml-maskrc/issues
GPLv2: https://github.com/kwongj/cfml-maskrc/blob/master/LICENSE